All File Changes

v254_preview2 to v254_base (2011-07-12 to 2011-07-19) v254

• python/lib/ucscgenomics/softfile/SoftFile.py
  • lines changed 51, context: html, text, full: html, text
    added new version of soft file to allow for micro array data
• python/programs/mkGeoPkg/mkGeoPkg
  • lines changed 25, context: html, text, full: html, text
    cleaner version of mkGeoPkg
  • lines changed 108, context: html, text, full: html, text
    added new version of soft file to allow for micro array data
• src/hg/encode/encodeExp/encodeExp
  • lines changed 20919, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/foo.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/hg18.in.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/hg18.new.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/hg18.newest.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/hg19.dump
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/hg19.found.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/hg19.in.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/hg19.new.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/hg19.newest.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/hg19.out.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/hg19.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/hg19.tues.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/hg19.txt
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/meta.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/mm9.9pm.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/mm9.in.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/mm9.new.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/mm9.newest.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/mm9.tues.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/new.out.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/old.out.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/out.ra
  • lines changed 14984, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/out.txt
  • lines changed 1873, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/junk/test.ra
  • lines changed 21, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/tags
  • lines changed 37, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/encode/encodeExp/temp.ra
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    Merging with origin
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    Removing junk
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 1, context: html, text, full: html, text
    added bedRnaElements
• src/hg/encode/encodeMkGeoPkg/ucsc_encode_dcc_wgEncodeCaltechRnaSeq.soft
  • lines changed 1733, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/encode/encodeRenameObj/encodeRenameObj.c
  • lines changed 6, context: html, text, full: html, text
    checks that length of newObj does not exceed mysql table limit of 64 chars
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 26, context: html, text, full: html, text
    marked up some more comments and removed deprecated lines from doEncodeValidate
• src/hg/encode/hgEncodeMatrix/hgEncodeMatrix.c
  • lines changed 196, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/encode/hgEncodeSubmit/config/database.yml
  • lines changed 81, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/encode/hgEncodeSubmit/config/environment.rb
  • lines changed 92, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/encode/hgEncodeSubmit/go
  • lines changed 2, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/encode/hgEncodeSubmit/stop
  • lines changed 3, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/hgGateway/tags
  • lines changed 18, context: html, text, full: html, text
    Merging with origin
  • lines changed 18, context: html, text, full: html, text
    Removing junk
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 39, context: html, text, full: html, text
    make it so unlisted hubs don't disappear when you deselect them, and add the ability to disconnect them
  • lines changed 12, context: html, text, full: html, text
    fixes to problems in #4627
• src/hg/hgTracks/hgTracks.c
  • lines changed 23, context: html, text, full: html, text
    add IN_PLACE_UPDATE code (currently on live in larrym's tree
  • lines changed 21, context: html, text, full: html, text
    Reworking measureTiming messages so that parallel time is visible and a few other time consuming things are more obvious.
• src/hg/hgTracks/imageV2.h
  • lines changed 1, context: html, text, full: html, text
    add IN_PLACE_UPDATE code (currently on live in larrym's tree
• src/hg/hgc/gencodeClick.c
  • lines changed 2, context: html, text, full: html, text
    move GENCODE tags section up in display since it can be very useful
  • lines changed 28, context: html, text, full: html, text
    added links to obtain predicted sequences for GENCODE genes
• src/hg/hgc/hgc.c
  • lines changed 56, context: html, text, full: html, text
    Refined details page for COSMIC track.
• src/hg/htdocs/ENCODE/dataMatrix/sav
  • lines changed 76, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 4, context: html, text, full: html, text
    adding gencode genes V7
  • lines changed 4, context: html, text, full: html, text
    adding HAIB TFBS, redmine# 70
• src/hg/htdocs/ENCODE/index.html
  • lines changed 105, context: html, text, full: html, text
    Add June and July news items
  • lines changed 4, context: html, text, full: html, text
    Add Usage Resources page to portal
  • lines changed 1, context: html, text, full: html, text
    modified Kate's portal page: changed link name, title, sections and removed bad html. Redmine# 4453
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 45, context: html, text, full: html, text
    Add June and July news items
• src/hg/htdocs/ENCODE/usageResources.html
  • lines changed 73, context: html, text, full: html, text
    Add Usage Resources page to portal
  • lines changed 17, context: html, text, full: html, text
    modified Kate's portal page: changed link name, title, sections and removed bad html. Redmine# 4453
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 75, context: html, text, full: html, text
    Added FAQ for explanation of 4th BED column, Redmine #4310
  • lines changed 6, context: html, text, full: html, text
    Made a few minor fixes
  • lines changed 7, context: html, text, full: html, text
    Made a couple more minor fixes
  • lines changed 8, context: html, text, full: html, text
    Fixed line breaks
  • lines changed 5, context: html, text, full: html, text
    Removed extra lines
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    Added </PRE> end tag
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    Removed extra line break
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 230, context: html, text, full: html, text
    Adding several ENCODE formats
  • lines changed 104, context: html, text, full: html, text
    Adding more ENCODE data formats
  • lines changed 8, context: html, text, full: html, text
    Updated score description to be 0-1000
  • lines changed 2, context: html, text, full: html, text
    Emphasized the deprication of tagAligns
• src/hg/htdocs/Neandertal/index.html
  • lines changed 77, context: html, text, full: html, text
    MLQ #4480: Adding links to hg19 download files to the Neandertal portalpage, since Brooke noticed they were missing.
• src/hg/htdocs/goldenPath/help/hgCodonColoring.html
  • lines changed 1, context: html, text, full: html, text
    cyan text never turns into cyan lines
• src/hg/htdocs/images/floretPreview.kuhn.jpg
  • lines changed 253, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    Updating date on ucsc genes announcement.
  • lines changed 1, context: html, text, full: html, text
    Removing quotes.
  • lines changed 84, context: html, text, full: html, text
    Fixing merge conflict, hopefully no new edits.
  • lines changed 1, context: html, text, full: html, text
    Adding : for format consistency
• src/hg/htdocs/style/hgHubConnect.css
  • lines changed 13, context: html, text, full: html, text
    made lots of tweaks in the css for better display and to fix some issues.
  • lines changed 1, context: html, text, full: html, text
    Added some padding to teh top of the tabs section so that the text above it (genome: human, etf, was not sitting right on top of it.
• src/hg/inc/hubConnect.h
  • lines changed 8, context: html, text, full: html, text
    make it so unlisted hubs don't disappear when you deselect them, and add the ability to disconnect them
  • lines changed 3, context: html, text, full: html, text
    oops.. these are part of the fixes for #4627
• src/hg/inc/trackHub.h
  • lines changed 5, context: html, text, full: html, text
    move hubCheck utility to library, fix up some error messages, facilitate using hubCheck as a hub crawler called from cron to validate public hubs.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v254
• src/hg/js/ajax.js
  • lines changed 11, context: html, text, full: html, text
    more work on in-place updating
• src/hg/js/hgTracks.js
  • lines changed 12, context: html, text, full: html, text
    more work on in-place updating
• src/hg/lib/TAGS
  • lines changed 28029, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/lib/encode/encodeExp.c
  • lines changed 21, context: html, text, full: html, text
    Allow Control terms for Antibody type (non-canonical validation of term for type -- should eventually go into cv.c
  • lines changed 21, context: html, text, full: html, text
    Merging with origin
• src/hg/lib/hubConnect.c
  • lines changed 55, context: html, text, full: html, text
    make it so unlisted hubs don't disappear when you deselect them, and add the ability to disconnect them
  • lines changed 5, context: html, text, full: html, text
    oops.. these are part of the fixes for #4627
• src/hg/lib/jsHelper.c
  • lines changed 4, context: html, text, full: html, text
    make jsPrintHash print json compliant output
• src/hg/lib/make.out
  • lines changed 71, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/lib/mdb.c
  • lines changed 1, context: html, text, full: html, text
    Allow Control terms for Antibody type (non-canonical validation of term for type -- should eventually go into cv.c
  • lines changed 1, context: html, text, full: html, text
    Too much information
• src/hg/lib/pgSnp.c
  • lines changed 1, context: html, text, full: html, text
    MLQ #4606: user found that a two-base deletion was not recognized asa frameshift by pgSnp hgc handler. Fix: since dnaseq.c's translateSeq returns a protein with empty sequence if the input is less than 3 bases (like "-G"), check for emtpy sequence. I kind of wonder if translateSeq should return "X" if the input is 1 or 2 bases...?
• src/hg/lib/stash/exp/mdb.c
  • lines changed 3419, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/lib/tags
  • lines changed 30974, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    move hubCheck utility to library, fix up some error messages, facilitate using hubCheck as a hub crawler called from cron to validate public hubs.
• src/hg/lib/trackHub.c
  • lines changed 114, context: html, text, full: html, text
    move hubCheck utility to library, fix up some error messages, facilitate using hubCheck as a hub crawler called from cron to validate public hubs.
• src/hg/makeDb/doc/cavPor3.txt
  • lines changed 14, context: html, text, full: html, text
    adding liftOver from cavPor3 to hg19
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release1.notes
  • lines changed 6, context: html, text, full: html, text
    removbed files that I accidently restored through a git error from back in the day.
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    Updated with dropped files
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes
  • lines changed 1361, context: html, text, full: html, text
    Finishing touches on track, a new notes file, a new .html file with release notes and the new views described
• src/hg/makeDb/doc/hg19.txt
  • lines changed 189, context: html, text, full: html, text
    running the fosEnd build and patch5 is complete
  • lines changed 6, context: html, text, full: html, text
    patch5 tracks done for hg19 and blat server turned on for hg19Patch5
  • lines changed 30, context: html, text, full: html, text
    Added COSMIC track.
• src/hg/makeDb/doc/hg19Patch5.txt
  • lines changed 167, context: html, text, full: html, text
    completed hg19Patch5 build and alignments to hg19
  • lines changed 15, context: html, text, full: html, text
    patch5 tracks done for hg19 and blat server turned on for hg19Patch5
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 23, context: html, text, full: html, text
    adding hg19Patch5
• src/hg/makeDb/mdbUpdate/tests/output/chipSeqTest1.ra
  • lines changed 191, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/makeDb/mdbUpdate/tests/output/expTest1.ra
  • lines changed 7, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/makeDb/trackDb/cv/alpha/.cv.ra.swp
  • lines changed 19, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Trimmed descriptions to suitable length
  • lines changed 7, context: html, text, full: html, text
    added provisional exonsgencv7 term
  • lines changed 12, context: html, text, full: html, text
    Adding terms for V7 Gencode
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    This is in repsonse to code review 4578 and 4579. I took out some provisional tags, changed a tab typo, removed some cruft
  • lines changed 4, context: html, text, full: html, text
    Added protocol links for Placenta and Limb provided by Ren lab. Fixes Redmine #315.
  • lines changed 2, context: html, text, full: html, text
    Fixed label for protocol to be Pi name, rather than lab name.
  • lines changed 3, context: html, text, full: html, text
    Updated HSMM and HSMMT description an venderID
  • lines changed 4, context: html, text, full: html, text
    Replacing TSS with TssGencV7 so that we specify the version from here on out
  • lines changed 5, context: html, text, full: html, text
    Adding new readType 2x76D
  • lines changed 6, context: html, text, full: html, text
    Added in a TssGencV3c as well as the V7 added earlier
• src/hg/makeDb/trackDb/cv/alpha/cv.tier2.5.ra
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    Merging with origin
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    Removing junk
• src/hg/makeDb/trackDb/cv/alpha/junk/cv.txt
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    Merging with origin
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    Removing junk
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 324, context: html, text, full: html, text
    pushing cv.ra to public, redmine# 4579
• src/hg/makeDb/trackDb/human/encodeEgaspFull.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to Brent Lab
• src/hg/makeDb/trackDb/human/encodeUvaDnaRepTr50.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to Dutta Lab
• src/hg/makeDb/trackDb/human/hg18/encodeUppsalaChip.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to Claes Wadelius Lab
• src/hg/makeDb/trackDb/human/hg18/encodeUppsalaChipBut.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to Claes Wadelius Lab
• src/hg/makeDb/trackDb/human/hg18/encodeUppsalaChipSuper.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to Claes Wadelius Lab
• src/hg/makeDb/trackDb/human/hg18/encodeYaleChipRfbr.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to Efron publication
• src/hg/makeDb/trackDb/human/hg18/encodeYaleChipSuper.html
  • lines changed 2, context: html, text, full: html, text
    Fixed broken links for Cawly and Efron publications
• src/hg/makeDb/trackDb/human/hg18/knownGene.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to UniProt
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • lines changed 2, context: html, text, full: html, text
    Fixed broken links to Quake publication and SNPs download file
• src/hg/makeDb/trackDb/human/hg18/uppsalaChipSignal.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link for Claes Wadelius Lab
• src/hg/makeDb/trackDb/human/hg18/uppsalaChipSites.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link for Claes Wadelius Lab
• src/hg/makeDb/trackDb/human/hg18/uppsalaChipSuper.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link for Claes Wadelius Lab
• src/hg/makeDb/trackDb/human/hg19/altSeqComposite2.ra
  • lines changed 104, context: html, text, full: html, text
    move the altSeqComposite into separate files to allow update to patch5
• src/hg/makeDb/trackDb/human/hg19/altSeqComposite5.ra
  • lines changed 104, context: html, text, full: html, text
    move the altSeqComposite into separate files to allow update to patch5
• src/hg/makeDb/trackDb/human/hg19/junk/boo
  • lines changed 56, context: html, text, full: html, text
    Merging with origin
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    Removing junk
• src/hg/makeDb/trackDb/human/hg19/junk/showStatus.csh
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    Merging with origin
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    Removing junk
• src/hg/makeDb/trackDb/human/hg19/junk/temp
  • lines changed 12, context: html, text, full: html, text
    Merging with origin
  • lines changed 12, context: html, text, full: html, text
    Removing junk
• src/hg/makeDb/trackDb/human/hg19/junk/temp.txt
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    Merging with origin
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    Removing junk
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 161, context: html, text, full: html, text
    changed dates for dateUnrestricted according to redmine 4331
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    removed fileIndex field
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 245, context: html, text, full: html, text
    Changed .gz to .tgz for paired fastqs, removed V2 where added erroneously, added origAssmbly where added erroneously, trying to remove md5sums for the paired fastqs
  • lines changed 35, context: html, text, full: html, text
    Changed TSS to TssGencV3c for clarification
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    updated CshlLongRnaSeq to reflect submission # from geo
  • lines changed 4201, context: html, text, full: html, text
    added a lot of cshl long tracks
  • lines changed 5, context: html, text, full: html, text
    removed fileIndex field
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    Adding 4 submissions with the V7 files
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 1199, context: html, text, full: html, text
    added a lot of subtracks to cshl short rna seq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 5, context: html, text, full: html, text
    Removed replicate pooled
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 166, context: html, text, full: html, text
    removed fileIndex field
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 79, context: html, text, full: html, text
    removed fileIndex field
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
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    removed fileIndex field
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 41, context: html, text, full: html, text
    removed fileIndex field
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 600, context: html, text, full: html, text
    replacing Riken TSS with Riken TSS GencV7
  • lines changed 89, context: html, text, full: html, text
    Finishing touches on track, a new notes file, a new .html file with release notes and the new views described
  • lines changed 2, context: html, text, full: html, text
    Remove fileiIndex
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 7, context: html, text, full: html, text
    commit hand made changes before i try out my script to mass change dates for a large paper
  • lines changed 28, context: html, text, full: html, text
    forgot to commit histone changes for K562b
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 173, context: html, text, full: html, text
    changed treatment to tnfa for experiment that were incorrect
  • lines changed 129, context: html, text, full: html, text
    loaded mdb for 4412, it was missing earlier
  • lines changed 385, context: html, text, full: html, text
    added in some missing meta data
  • lines changed 137, context: html, text, full: html, text
    removed K562b traces
  • lines changed 21, context: html, text, full: html, text
    changed control for gm12878 nfkb form std to iggrab
  • lines changed 78, context: html, text, full: html, text
    changed files names for adding iggrab to gm12878 nfkb
  • lines changed 489, context: html, text, full: html, text
    cleaned up a lot of stuff in sydh tfbs per redmine #69
  • lines changed 68, context: html, text, full: html, text
    commit hand made changes before i try out my script to mass change dates for a large paper
  • lines changed 8, context: html, text, full: html, text
    moved k562/mnased/setdb1 to release 2 also found one last k562b that i missed somehow
  • lines changed 86, context: html, text, full: html, text
    correct a typing error TFNa > TNFa
  • lines changed 42, context: html, text, full: html, text
    corrected some control errors, more to go
  • lines changed 8, context: html, text, full: html, text
    renamed mislabeled control
  • lines changed 127, context: html, text, full: html, text
    fixed metadata control issues
  • lines changed 100, context: html, text, full: html, text
    fixed even more metadata control issues, name changes in this one too
  • lines changed 158, context: html, text, full: html, text
    forgot to add tnfa to gm12878
  • lines changed 203, context: html, text, full: html, text
    reverted previous commit, it was done in error
  • lines changed 1977, context: html, text, full: html, text
    added dccaccesion expId's where missing and changed controlId over to dcc accession
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 2, context: html, text, full: html, text
    added geo Series number
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 98, context: html, text, full: html, text
    removed fileIndex field
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 2, context: html, text, full: html, text
    staging HAIB TFBS on beta, redmine #70
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibTfbs.ra
  • lines changed 42681, context: html, text, full: html, text
    staging HAIB TFBS on beta, redmine #70
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    releasing HAIB TFBS, redmine# 70
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibTfbs.ra
  • lines changed 42681, context: html, text, full: html, text
    releasing HAIB TFBS, redmine# 70
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    changed anoCar1 to anoCar2 in the vertebrate composite chain-net track so that the track appears in the vert track and not on its own
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    adding altSeqCompositeP5 and hg19FosEnd pairs tracks
  • lines changed 2, context: html, text, full: html, text
    distinguish patch 5 GRC Patch Release track labels
  • lines changed 209, context: html, text, full: html, text
    move the altSeqComposite into separate files to allow update to patch5
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    staging HAIB TFBS on beta, redmine #70
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
  • lines changed 13, context: html, text, full: html, text
    added references to the pages according to redmine 4331
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 1, context: html, text, full: html, text
    Changed fileSortOrder
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Removed the numbers from the begeinning of the labels
  • lines changed 1014, context: html, text, full: html, text
    added a lot of cshl long tracks
  • lines changed 60, context: html, text, full: html, text
    subgroups didn't have pooled, but patchtdb didn't throw error
  • lines changed 8, context: html, text, full: html, text
    a previous search and replace error made chromatin > chromatim, corrected
  • lines changed 1, context: html, text, full: html, text
    mispelling in short label
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 437, context: html, text, full: html, text
    added a lot of subtracks to cshl short rna seq
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.html
  • lines changed 9, context: html, text, full: html, text
    corrected some errors in haib tfbs's html
  • lines changed 1, context: html, text, full: html, text
    fixed a word
  • lines changed 10, context: html, text, full: html, text
    added a period, redmine#70
  • lines changed 2, context: html, text, full: html, text
    updated section titles, redmine#70
  • lines changed 2, context: html, text, full: html, text
    updated section title and the reference to it, redmine#70
  • lines changed 2, context: html, text, full: html, text
    decided against the updated section title and the reference to it, redmine#70
  • lines changed 47, context: html, text, full: html, text
    moved protocols to be within the methods section, redmine#70
  • lines changed 8, context: html, text, full: html, text
    correct some html errors
  • lines changed 1, context: html, text, full: html, text
    changed a word
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra
  • lines changed 1, context: html, text, full: html, text
    Updated the fileSortOrder to put the order of importance of variables and to match other tracks.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated the fileSortOrder to put the order of importance of variables and to match other tracks.
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    changed supertrack view for haib to dense
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.html
  • lines changed 141, context: html, text, full: html, text
    Finishing touches on track, a new notes file, a new .html file with release notes and the new views described
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
  • lines changed 1, context: html, text, full: html, text
    Finishing touches on track, a new notes file, a new .html file with release notes and the new views described
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html
  • lines changed 10, context: html, text, full: html, text
    added references to the pages according to redmine 4331
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
  • lines changed 21, context: html, text, full: html, text
    added references to the pages according to redmine 4331
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 34, context: html, text, full: html, text
    changed files names for adding iggrab to gm12878 nfkb
  • lines changed 143, context: html, text, full: html, text
    cleaned up a lot of stuff in sydh tfbs per redmine #69
  • lines changed 16, context: html, text, full: html, text
    moved k562/mnased/setdb1 to release 2 also found one last k562b that i missed somehow
  • lines changed 5, context: html, text, full: html, text
    changed name for mislabeled control
  • lines changed 27, context: html, text, full: html, text
    added missing TNFa treatments to subgroups and labels
  • lines changed 18, context: html, text, full: html, text
    fixed even more metadata control issues, name changes in this one too
  • lines changed 5, context: html, text, full: html, text
    forgot to add tnfa to gm12878
  • lines changed 5, context: html, text, full: html, text
    reverted previous commit, it was done in error
  • lines changed 1, context: html, text, full: html, text
    put in filesort order for sydh tfbs, mainly a placeholder
  • lines changed 1, context: html, text, full: html, text
    corrected a typing error
• src/hg/makeDb/trackDb/human/hg19/wgEncodeTfBindingSuper.html
  • lines changed 4, context: html, text, full: html, text
    Temporary ad for Previw browser (will be replaced by hgTrackUi note after next release)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 1, context: html, text, full: html, text
    added geo accession sort field
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    Added search term for COSMIC.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 343, context: html, text, full: html, text
    Fixed meta-data with MEL cell line. Dsiplaying 2 experiments that were loaded correctly and fixed trackDb. All in response to Mouse ENCODE 101 Paper.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 11, context: html, text, full: html, text
    Fixed meta-data with MEL cell line. Dsiplaying 2 experiments that were loaded correctly and fixed trackDb. All in response to Mouse ENCODE 101 Paper.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.html
  • lines changed 135, context: html, text, full: html, text
    Added track Description. Redmine #829.
• src/hg/pslPairs/pslPairs.c
  • lines changed 80, context: html, text, full: html, text
    modernize to newer style of kent code
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 81, context: html, text, full: html, text
    move hubCheck utility to library, fix up some error messages, facilitate using hubCheck as a hub crawler called from cron to validate public hubs.
• src/inc/sav/common.mk
  • lines changed 201, context: html, text, full: html, text
    Merging with origin
  • lines changed 201, context: html, text, full: html, text
    Removing junk
• src/lib/htmshell.c
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    Strange trick to avoid FF back button issue.
• src/lib/tests/makefile
  • lines changed 4, context: html, text, full: html, text
    Adding target for udcTest in lib/tests, but *not* hooking it up totop-level "make test". Also adding udcTrials.csh that runs udcTest many times interspersed w/sleeps.
• src/lib/tests/udcTrials.csh
  • lines changed 15, context: html, text, full: html, text
    Adding target for udcTest in lib/tests, but *not* hooking it up totop-level "make test". Also adding udcTrials.csh that runs udcTest many times interspersed w/sleeps.
• src/makefile
  • lines changed 2, context: html, text, full: html, text
    add hubCheck to userApps (#4526)
• src/makelibs.out
  • lines changed 119, context: html, text, full: html, text
    Merging with origin
  • lines changed 119, context: html, text, full: html, text
    Removing junk
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v254 final build

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• files changed: 288